Assignment_6_JH_GE

Introduction

Figure 1. Pacific Giant Salamander (Credit: Sierra Nystrom)

Figure 2. The Mack Creek study site is located in the HJ Andrews Experimental Forest, Oregon. (Credit: Dana Warren)

Figure 3. Mack Creek, HJ Andrews Experimental Forest, OR (Credit: Oregon State University)

Data and Methods

Results

Channel Class	Clear Cut	Old Growth
Cascade	247 (55%)	201 (45%)
Pool	31 (41%)	45 (59%)
Side Channel	90 (55%)	74 (45%)

## 
##  Pearson's Chi-squared test
## 
## data:  chi_sal_counts
## X-squared = 5.5413, df = 2, p-value = 0.06262

There is not a significant association between forest condition (old growth/clear cut) on where in the channel salamanders are found (pool/side-channel/cascade) for salamanders sampled in 2017. (\(\chi\)²(2) = 5.54, p = 0.063).

## 
##  Welch Two Sample t-test
## 
## data:  weight_ttest_og and weight_ttest_cc
## t = -1.6669, df = 692.79, p-value = 0.09599
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
##  -2.5972032  0.2121307
## sample estimates:
## mean of x mean of y 
##  6.583333  7.775870

## 
## Cohen's d
## 
## d estimate: 0.1259284 (negligible)
## 95 percent confidence interval:
##      lower      upper 
## -0.0234303  0.2752870

There is not enough evidence to conclude that mean Pacific Giant Salamander size in the clear cut section of Mack Creek in 2017 (7.78 \(\pm\) 9.9, n = 368) differed significantly from mean Pacific Giant Salamander size in the old growth section of Mack Creek in 2017 (6.58 \(\pm\) 8.96, n = 327) by a two-sided, two sample t-test (t(692.79) = -1.67, p = 0.096). In addition, the effect size between mean sizes is negligible (Cohen’s d = 0.13).

## Levene's Test for Homogeneity of Variance (center = median)
##        Df F value  Pr(>F)  
## group   2  2.3883 0.09255 .
##       684                  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

##                Df Sum Sq Mean Sq F value Pr(>F)  
## channel_class   2    757   378.4   4.216 0.0151 *
## Residuals     684  61403    89.8                 
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 1 observation deleted due to missingness

## Anova Table (Type II tests)
## 
## Response: weight
##               Sum Sq  Df F value  Pr(>F)  
## channel_class    757   2  4.2156 0.01515 *
## Residuals      61403 684                  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

##   Tukey multiple comparisons of means
##     95% family-wise confidence level
## 
## Fit: aov(formula = weight ~ channel_class, data = sal_weights_class)
## 
## $channel_class
##                           diff        lwr        upr     p adj
## Pool-Cascade          1.776650 -0.9846147  4.5379145 0.2862119
## Side Channel-Cascade -1.844204 -3.8759182  0.1875106 0.0841989
## Side Channel-Pool    -3.620854 -6.7089770 -0.5327303 0.0166225

## Call:
##    aov(formula = weight ~ channel_class, data = sal_weights_class)
## 
## Terms:
##                 channel_class Residuals
## Sum of Squares         756.87  61403.22
## Deg. of Freedom             2       684
## 
## Residual standard error: 9.474745
## Estimated effects may be unbalanced
## 1 observation deleted due to missingness

## 
## Cohen's d
## 
## d estimate: 0.2088538 (small)
## 95 percent confidence interval:
##      lower      upper 
## 0.02917986 0.38852765

Mean salamander weight (g) differed significantly between the side-channel and pool channel classifications (one-way ANOVA with post-hoc Tukey’s HSD, F(2, 684) = 4.22, p = 0.015). Although mean salamander weight differed significantly, the effect size is small (Cohen’s d = 0.21).

Summary

References

Gregory S. V. 2016. Aquatic Vertebrate Population Study in Mack Creek, Andrews Experimental Forest, 1987 to present. Environmental Data Initiative. https://doi.org/10.6073/pasta/5de64af9c11579266ef20da2ff32f702. Dataset accessed 11/27/2019.